[Insight-users] Re: incorrect z-spacing in GDCM reading

[Miller, James V (Research)]

Mathieu, 

We have a use case where this happens that we were discussing today.  If your create 
DICOM images from scratch (i.e. not reading a DICOM but are producing a DICOM) or 
you are not sharing an instance of GDCMImageIO between the input and the output, then
the z position in ImagePositionPatient will be incorrect.

The problem is that the ImageSeriesWriter is given an 3D image.  It then uses an
ImageFileWriter to write each slice (a 2D image). When ImageFileWriter only "sees"
a 2D image, therefore there is not 3rd coordinate to give to GDCMImageIO to set 
the Z position of the image position patient.

You could invision a solution where information is passed to GDCMImageIO via 
the meta data dictionary.  While GDCMImageIO does take information from the 
dictionary, some of the tags are always overridden by GDCMImageIO. It is some 
of these tags that keep you from specifying the correct Z coordinate of the ImagePositionPatient.

As a temporary workaround we commented out where GDCMImageIO sets ImagePositionPatient
and assume it was set in the meta data dictionary.

Jim



-----Original Message-----
From: insight-users-bounces+millerjv=crd.ge.com at itk.org
[mailto:insight-users-bounces+millerjv=crd.ge.com at itk.org]On Behalf Of
Mathieu Malaterre
Sent: Wednesday, May 11, 2005 4:45 PM
To: Hxsham Fire
Cc: insight-users at itk.org
Subject: Re: [Insight-users] Re: incorrect z-spacing in GDCM reading


Hxsham

	What are you reporting is rather scary. Could you tell us which version 
of ITK are you using ? Also on which example did you base your code ? 
The fact is that this is tested nightly:

$ ctest -R itkGDCMSeriesReadImageWrite -V

This create three new files in Testing/Temporary/. Then all you need to 
check is that 'Image Position Patient' is correct:


$ for i in `ls Testing/Temporary/*.dcm`; do 
./bin/DicomImageReadPrintTags $i; done | grep "Image Position"

Image Position Patient = -112\ -21.688\ 126.894
Image Position Patient = -112\-20.2729\ 127.641
Image Position Patient = -112\-18.8578\ 128.388

	Which looks good to me...

HTH,
Mathieu

Hxsham Fire wrote:
> George and Mathieu,
> 
> This looks very similar to the problem I was having
> with ITK...
> The dicom series reader was reading the slices fine,
> and the volume had correct spacing... however after I
> write the series using the dicom series writer and try
> to read it back again, for further modification is
> when the z spacing fails, and the slices are compacted
> in the z direction, and it is most noticable if I try
> to rotate that image...  also I noticed that all the
> slices have the same z coordinate of the origin in the
> series written by the dicom writer (that is field
> 0020|0030) in the dicom directory, and it is the
> values of the last slice in the original series that
> is written on all the slices in the output series.
> 
> Hxsham
> 
> ----------------------------------------------------
> ----------------------------------------------------
> 
> George,
> 
>         Your code looks fine. The algorithm for
> finding the z spacing is kind 
> of tricky. So I am wondering if:
> 
> 1. Your images might not have proper 'Image Position
> Patient' / 'Image 
> Orientation Patient'
> 
> 2. If they have, maybe gdcm is not able to parse the
> string properly.
> 
> Could it be possible that you send me at least two
> images from this 
> dataset ?
> 
> If not, you'll have to turn the code to be more
> verbose in particular 
> when entering the function:
> 
> 
>      gdcm::SerieHelper::ImagePositionPatientOrdering
> 
> Thanks,
> Mathieu
> 
> 
> 
> 		
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